Posted by
Stephan Saalfeld on
Nov 19, 2013; 12:09pm
URL: http://imagej.273.s1.nabble.com/trakem2-save-aligned-tif-images-as-movie-tp5005565p5005600.html
Hi Mandy,
you right click the canvas, do
Export -> Make Flat Image
Choose the scale and background color of your series and either show or
save it as a series of tiff files. You can then use Fiji/ImageJ to
convert this stack into an avi container that would play in most
players. Or you use avconv/ffmpeg if you want to be fancy ;), e.g.:
avconv -r 20 -i %04d.tif -f mov -vcodec libx264 -b 9600k movie.mov
Generates a 20fps h.264-compressed movie at ~9600k bitrate in a
quicktime mov container from a series of tif files that are numbered
0000.tif
0001.tif
0002.tif ...
Best,
Stephan
On Thu, 2013-11-14 at 09:26 -0800, mandue wrote:
> Hello everyone.
>
> I have some trouble using the trakem2 plugin.
>
> I used it to align tifs of serial sections.
> I now want to save this as a movie sequence (I do not care about the file
> format) but cannot find a way to do so...
> Also, I would be very thankful if one of you could give me a tip on how to
> crop all the aligned images in one go.
> And another question (sorry, I am completely new to this program :P ): if I
> want to change the rotation of all the aligned images in one go, how best to
> do it?
>
> Thank you very much for your replies! !!!
> cheers,
> mandy
>
>
>
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